Broman KW (2022) A generic hidden Markov model for multi-parent populations. G3 (Bethesda) 12:jkab396

Figure 1. — Illustration of genotype reconstruction in a 1 Mbp region in a single Diversity Outbred (DO) mouse. a. Genotypes of eight founder strains at a set of SNPs, with open and closed circles corresponding to being homozygous for the more-frequent and less-frequent allele, respectively. b. Genotype of the DO mouse at the SNPs, with gray indicating the mouse is heterozygous. c. Genotype probabilities for the DO mouse along the chromosome segment, given the observed data. Genotypes other than the two shown have negligible probability across the region. d. Inferred haplotypes in the DO mouse.